The Tha Chin River Basin (central Thailand) faces major water quality problems. Among others, freshwater aquaculture was identified to be one of the pollution sources. This study looks at nutrient loads coming from freshwater aquaculture systems in the area. A model based on a material flow analysis was set up to quantify the loads to canals and rivers as well as to identify the key factors (parameters) that influence the system. The focus was placed on four different major cultivation systems. For all four considered systems, the amount of feed and nutrient concentrations in feed have the highest influence on the nutrient loads to the canal. Catfish (lat. Clarias batrachus) has the highest production in the area and is also the most intensive system. Catfish are mainly fed with low quality sea fish. These cultures require a lot of freshwater because of the intensive production. Nutrient loads coming from catfish ponds are the highest among the observed systems, with 10 (+/- 5) tons of nitrogen per batch and hectare and 3 (+/- 1) tons of phosphorous per batch and hectare. Snakehead (lat. Channa striatus) is produced in a similar way as catfish. The loads are in the same range as for catfish, but snakehead is cultured less frequently. Tilapia (lat. Oreochromis niloticus) is the second most produced species and covers 40% of the area used for aquaculture. Tilapia cultures are often mixed with a certain percentage of other fish species. Tilapia is either fed with artificial pellet feed or with manure from different livestock. The nitrogen load per batch for manure fed systems and pellet fed systems is in the same range; namely 0.3 (+/- 0.2) tons N/ha. For phosphorous, the load per batch from Tilapia feeding on pellet is ten times lower than that from feeding on manure (0.02 (+/- 0.02) t P/ha; 0.2 (+/- 0.2) t P/ha). The fourth system is the production of tiger shrimp (lat. Panaeus monodon, P. vannamai), which covers 40% of the total aquaculture production area. The loads coming from a hectare of shrimp production are in the same range as for tilapia (0.3 (+/- 0.2) tons N/ha; 0.02 (+/- 0.02) t P/ha). At the scale of the study area, catfish causes the highest loads on a very small production area (less than 5% of the total) compared to tilapia and shrimp production. However, this finding needs to be put into another perspective, since catfish cause similar loads as tilapia if they are calculated per ton of fish yield.